ILC3s select for RORγt⁺ Tregs and establish tolerance to intestinal microbiota

Abstract

Microbial colonization of the mammalian intestine elicits inflammatory or tolerogenic T cell responses, but the mechanisms controlling these distinct outcomes remain poorly understood and accumulating evidence indicates that aberrant immunity to intestinal microbiota is causally associated with infectious, inflammatory, and malignant diseases1–8. Here, we define a critical pathway controlling the fate of inflammatory versus tolerogenic T cells that are specific for the microbiota and express the transcription factor RORγt. We profiled all RORγt+ immune cells at single cell resolution from the intestine-draining lymph nodes of mice and reveal a dominant presence of Tregs and lymphoid tissue-induced (LTi)-like group 3 innate lymphoid cells (ILC3s), which co-localize at interfollicular regions. These ILC3s have interconverting potential with RORγt+ extrathymic Aire-expressing cells, abundantly express major histocompatibility complex class II, and are necessary and sufficient to promote microbiota-specific RORγt+ Tregs and prevent their expansion as inflammatory T helper (Th)17 cells. This occurs through ILC3-mediated antigen-presentation, interleukin-2 gradients, and αv integrin. Finally, single-cell analyses demonstrate that ILC3 and RORγt+ Treg interactions are impaired in inflammatory bowel disease. Our results define a novel paradigm whereby ILC3s positively select for antigen specific RORγt+ Tregs, and against Th17 cells, to establish immune tolerance to the microbiota and intestinal health.

A novel RORγt+ antigen presenting cell type instructs microbiota-dependent regulatory T cell differentiation and tolerance during early life

“…Moreover, a recent report demonstrated IL7R ‘fate-mapping’ in ∼25% of cDCs 36 , precluding this approach as a means of lymphoid cell lineage tracing. Thus, while Aire + TC I represent RORγt + Aire + CCR6 + /Siglec-G + cells (referred to either as ‘Janus cells’ or RORγt + extrathymic Aire-expressing cells (eTACs) in two concurrent analyses of RORγt + APCs 34,35 ), TC II-IV described herein extend the spectrum of non-ILC3 RORγt + MHCII + cells beyond Aire-expressing cells ( Fig. 3l ).…”

“…3j,k). Of note, CCR6 and Siglec-G, suggested to be markers for RORgt + Aire + cells 15,34,35 , were expressed by TC I-II but not TC III-IV (Fig. 3i, Extended data Fig.…”

Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy

“…Among the genes with discordant species- and gene-expression phylogenies is RAR-related orphan receptor alpha ( RORA ), an orphan nuclear hormone receptor that regulates the development and function of type 2 and type 3 innate lymphoid cells (ILC2 and ILC3), which negatively regulates the immune system in local microenvironments especially during inflammation ( Haim-Vilmovsky et al, 2019 ), the establishment of tolerance to intestinal microbiota ( Lyu et al, 2022 ), and the regulation of inflammatory responses and vascular remodeling during placentation and pregnancy ( Balmas et al, 2018 ; Mendes et al, 2020 ; Miller et al, 2018 ). Remarkably, RORA independently lost endometrial expression at least four times, each loss coincident with the independent evolution of non-invasive epitheliochorial placentas ( Figure 5A ).…”